Their race on Geneva's mini- wooden bowl was their first track clash since Obree beat the Olympic champion in the semi-finals of the world 4,000 metres pursuit championship in Norway in August.
The riders were feted from their arrival and beyond the frenzied finale where Obree turned revenge into repeat by just over two seconds, clocking a track record of 4min 28.69sec.
Boardman, who started in the opposite straight to his rival, closed fast in the first half as Obree fought to get his bigger gear turning. Once it was wound up the Scot began eating away at Boardman's advantage.
'I just burst myself over the last six laps,' the Scot said. 'I could not believe it when I saw Chris ahead of me in the corner of the track.'
Boardman seemed to be expecting it. 'I have not got the condition for such a race and Graeme is still really fast,' he said.
Revenge is normally reserved for the title finalist but matching the Britons brought together men who in 12 months have taken cycling by storm with their innovative machinery which has produced four world records, an Olympic and a world title.
The pre-race atmosphere was heightened as the stadium was plunged into darkness, punctuated by the heavy beat of rock, then spotlights that searched the arena before falling on the protagonists.
Obree wants to retake the world hour record that Boardman lifted from him in July. It could happen next June. 'I cannot let it go so easily,' Obree said. 'I will attempt it at sea level as Chris did.'
He is hoping soon to take a break from a five-week spell 'on the road' that has taken the Scot to four countries and improved the bank balance of a man who might well still have been out of work but for a home-made bike and a riding posture that was once ridiculed but is now being tested seriously by other leading riders.Reuse content